Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.

ABSTRACT: Proteins are complex biomolecules which perform critical tasks in living organisms. Knowledge of a protein's structure is essential for understanding its physiological function in detail. Despite the incredible progress in experimental techniques, protein structure determination is still expensive, time-consuming, and arduous. That is why computer simulations are often used to complement or interpret experimental data. Here, we explore how in silico protein structure determination based on replica-exchange molecular dynamics (REMD) can benefit from including contact information derived from theoretical and experimental sources, such as direct coupling analysis or NMR spectroscopy. To reflect the influence from erroneous and noisy data we probe how false-positive contacts influence the simu

SUBMITTER: Voronin A 

PROVIDER: S-EPMC7668583 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature